update docs

remove duplication of sections of the docs, minor editing
SMTG-Bham · Mar 18, 2024 · 0ea5463 · 0ea5463
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diff --git a/docs/.doctrees/contents.doctree b/docs/.doctrees/contents.doctree
diff --git a/docs/.doctrees/environment.pickle b/docs/.doctrees/environment.pickle
diff --git a/docs/.doctrees/index.doctree b/docs/.doctrees/index.doctree
diff --git a/docs/.doctrees/tp.axes.doctree b/docs/.doctrees/tp.axes.doctree
diff --git a/docs/.doctrees/tp.cli.doctree b/docs/.doctrees/tp.cli.doctree
diff --git a/docs/.doctrees/tp.data.doctree b/docs/.doctrees/tp.data.doctree
diff --git a/docs/.doctrees/tp.doctree b/docs/.doctrees/tp.doctree
diff --git a/docs/.doctrees/tp.plot.doctree b/docs/.doctrees/tp.plot.doctree
diff --git a/docs/.doctrees/tp.setup.doctree b/docs/.doctrees/tp.setup.doctree
diff --git a/docs/_modules/index.html b/docs/_modules/index.html
@@ -44,7 +44,7 @@
 <li class="toctree-l1"><a class="reference internal" href="../index.html#contributors">Contributors</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../index.html#license">License</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../index.html#requirements">Requirements</a></li>
-<li class="toctree-l1"><a class="reference internal" href="../modules.html">Python Package</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../modules.html">Python API</a></li>
 </ul>
 
         </div>

diff --git a/docs/_modules/tp.html b/docs/_modules/tp.html
@@ -44,7 +44,7 @@
 <li class="toctree-l1"><a class="reference internal" href="../index.html#contributors">Contributors</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../index.html#license">License</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../index.html#requirements">Requirements</a></li>
-<li class="toctree-l1"><a class="reference internal" href="../modules.html">Python Package</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../modules.html">Python API</a></li>
 </ul>
 
         </div>
@@ -72,16 +72,16 @@
            <div itemprop="articleBody">
 
   <h1>Source code for tp</h1><div class="highlight"><pre>
-<span></span><span class="sd">&quot;&quot;&quot;Everything.</span>
+<span></span><span class="sd">&quot;&quot;&quot;A package for postprocessings transport calculations.&quot;&quot;&quot;</span>
 
-<span class="sd">Modules</span>
-<span class="sd">-------</span>
-
-<span class="sd">    calculate</span>
-<span class="sd">        tools for calculating derived properties and interpolating</span>
-<span class="sd">    settings</span>
-<span class="sd">        default values and metadata</span>
-<span class="sd">&quot;&quot;&quot;</span>
+<span class="c1">#Modules</span>
+<span class="c1">#-------</span>
+<span class="c1">#</span>
+<span class="c1">#    calculate</span>
+<span class="c1">#        tools for calculating derived properties and interpolating</span>
+<span class="c1">#    settings</span>
+<span class="c1">#        default values and metadata</span>
+<span class="c1">#&quot;&quot;&quot;</span>
 
 <div class="viewcode-block" id="docstring_replace"><a class="viewcode-back" href="../tp.html#tp.docstring_replace">[docs]</a><span class="k">def</span> <span class="nf">docstring_replace</span><span class="p">(</span><span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
     <span class="k">def</span> <span class="nf">d</span><span class="p">(</span><span class="n">f</span><span class="p">):</span>

diff --git a/docs/_modules/tp/axes/large.html b/docs/_modules/tp/axes/large.html
@@ -44,7 +44,7 @@
 <li class="toctree-l1"><a class="reference internal" href="../../../index.html#contributors">Contributors</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../../../index.html#license">License</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../../../index.html#requirements">Requirements</a></li>
-<li class="toctree-l1"><a class="reference internal" href="../../../modules.html">Python Package</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../../../modules.html">Python API</a></li>
 </ul>
 
         </div>
@@ -79,39 +79,40 @@ <h1>Source code for tp.axes.large</h1><div class="highlight"><pre>
 <span class="sd">axes and an add_legend function. The legend function comes with a</span>
 <span class="sd">choice of positions and takes normal ax.legend arguments. Drawing large</span>
 <span class="sd">figures is significantly slower than small ones.</span>
-
-<span class="sd">Functions</span>
-<span class="sd">---------</span>
-
-<span class="sd">    one</span>
-
-<span class="sd">    one_colourbar</span>
-
-<span class="sd">    one_dos</span>
-<span class="sd">    </span>
-<span class="sd">    one_dos_colourbar</span>
-<span class="sd">    </span>
-<span class="sd">    two_h</span>
-<span class="sd">    </span>
-<span class="sd">    two_h_colourbars</span>
-<span class="sd">    </span>
-<span class="sd">    two_v</span>
-<span class="sd">    </span>
-<span class="sd">    two_v_colourbars</span>
-<span class="sd">    </span>
-<span class="sd">    three_h</span>
-<span class="sd">    </span>
-<span class="sd">    three_h_colourbars</span>
-<span class="sd">    </span>
-<span class="sd">    three_square</span>
-<span class="sd">    </span>
-<span class="sd">    three_square_colourbars</span>
-<span class="sd">    </span>
-<span class="sd">    four_square</span>
-<span class="sd">    </span>
-<span class="sd">    four_square_colourbars</span>
 <span class="sd">&quot;&quot;&quot;</span>
 
+<span class="c1">#Functions</span>
+<span class="c1">#---------</span>
+<span class="c1">#</span>
+<span class="c1">#    one</span>
+<span class="c1">#</span>
+<span class="c1">#    one_colourbar</span>
+<span class="c1">#</span>
+<span class="c1">#    one_dos</span>
+<span class="c1">#    </span>
+<span class="c1">#    one_dos_colourbar</span>
+<span class="c1">#    </span>
+<span class="c1">#    two_h</span>
+<span class="c1">#    </span>
+<span class="c1">#    two_h_colourbars</span>
+<span class="c1">#    </span>
+<span class="c1">#    two_v</span>
+<span class="c1">#    </span>
+<span class="c1">#    two_v_colourbars</span>
+<span class="c1">#    </span>
+<span class="c1">#    three_h</span>
+<span class="c1">#    </span>
+<span class="c1">#    three_h_colourbars</span>
+<span class="c1">#    </span>
+<span class="c1">#    three_square</span>
+<span class="c1">#    </span>
+<span class="c1">#    three_square_colourbars</span>
+<span class="c1">#    </span>
+<span class="c1">#    four_square</span>
+<span class="c1">#    </span>
+<span class="c1">#    four_square_colourbars</span>
+<span class="c1">#&quot;&quot;&quot;</span>
+
 <span class="kn">import</span> <span class="nn">matplotlib.pyplot</span> <span class="k">as</span> <span class="nn">plt</span>
 <span class="kn">from</span> <span class="nn">matplotlib.gridspec</span> <span class="kn">import</span> <span class="n">GridSpec</span>
 <span class="kn">import</span> <span class="nn">tp</span>

diff --git a/docs/_modules/tp/axes/legend.html b/docs/_modules/tp/axes/legend.html
@@ -44,7 +44,7 @@
 <li class="toctree-l1"><a class="reference internal" href="../../../index.html#contributors">Contributors</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../../../index.html#license">License</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../../../index.html#requirements">Requirements</a></li>
-<li class="toctree-l1"><a class="reference internal" href="../../../modules.html">Python Package</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../../../modules.html">Python API</a></li>
 </ul>
 
         </div>
@@ -73,18 +73,18 @@
            <div itemprop="articleBody">
 
   <h1>Source code for tp.axes.legend</h1><div class="highlight"><pre>
-<span></span><span class="sd">&quot;&quot;&quot;Functions for dealing with legends.</span>
-
-<span class="sd">Functions</span>
-<span class="sd">---------</span>
-
-<span class="sd">    consolidate</span>
-<span class="sd">        combine legends.</span>
-<span class="sd">    add_add_legend</span>
-<span class="sd">        add add_legend function.</span>
-<span class="sd">    alphabetise</span>
-<span class="sd">        alphabetises or enumerates axes.</span>
-<span class="sd">&quot;&quot;&quot;</span>
+<span></span><span class="sd">&quot;&quot;&quot;Functions for dealing with legends.&quot;&quot;&quot;</span>
+
+<span class="c1">#Functions</span>
+<span class="c1">#---------</span>
+<span class="c1">#</span>
+<span class="c1">#    consolidate</span>
+<span class="c1">#        combine legends.</span>
+<span class="c1">#    add_add_legend</span>
+<span class="c1">#        add add_legend function.</span>
+<span class="c1">#    alphabetise</span>
+<span class="c1">#        alphabetises or enumerates axes.</span>
+<span class="c1">#&quot;&quot;&quot;</span>
 
 <span class="kn">import</span> <span class="nn">numpy</span> <span class="k">as</span> <span class="nn">np</span>
 <span class="kn">import</span> <span class="nn">tp</span>

diff --git a/docs/_modules/tp/axes/small.html b/docs/_modules/tp/axes/small.html
@@ -44,7 +44,7 @@
 <li class="toctree-l1"><a class="reference internal" href="../../../index.html#contributors">Contributors</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../../../index.html#license">License</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../../../index.html#requirements">Requirements</a></li>
-<li class="toctree-l1"><a class="reference internal" href="../../../modules.html">Python Package</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../../../modules.html">Python API</a></li>
 </ul>
 
         </div>
@@ -78,39 +78,40 @@ <h1>Source code for tp.axes.small</h1><div class="highlight"><pre>
 <span class="sd">Each function returns a figure, a set of axes or an array of sets of</span>
 <span class="sd">axes and an add_legend function. The legend function comes with a</span>
 <span class="sd">choice of positions and takes normal ax.legend arguments.</span>
-
-<span class="sd">Functions</span>
-<span class="sd">---------</span>
-
-<span class="sd">    one</span>
-<span class="sd">    </span>
-<span class="sd">    one_colourbar</span>
-<span class="sd">    </span>
-<span class="sd">    one_dos</span>
-<span class="sd">    </span>
-<span class="sd">    one_dos_colourbar</span>
-<span class="sd">    </span>
-<span class="sd">    two_h</span>
-<span class="sd">    </span>
-<span class="sd">    two_h_colourbars</span>
-<span class="sd">    </span>
-<span class="sd">    two_v</span>
-<span class="sd">    </span>
-<span class="sd">    two_v_colourbars</span>
-<span class="sd">    </span>
-<span class="sd">    three_h</span>
-<span class="sd">    </span>
-<span class="sd">    three_h_colourbars</span>
-<span class="sd">    </span>
-<span class="sd">    three_square</span>
-<span class="sd">    </span>
-<span class="sd">    three_square_colourbars</span>
-<span class="sd">    </span>
-<span class="sd">    four_square</span>
-<span class="sd">    </span>
-<span class="sd">    four_square_colourbars</span>
 <span class="sd">&quot;&quot;&quot;</span>
 
+<span class="c1">#Functions</span>
+<span class="c1">#---------</span>
+<span class="c1">#</span>
+<span class="c1">#    one</span>
+<span class="c1">#    </span>
+<span class="c1">#    one_colourbar</span>
+<span class="c1">#    </span>
+<span class="c1">#    one_dos</span>
+<span class="c1">#    </span>
+<span class="c1">#    one_dos_colourbar</span>
+<span class="c1">#    </span>
+<span class="c1">#    two_h</span>
+<span class="c1">#    </span>
+<span class="c1">#    two_h_colourbars</span>
+<span class="c1">#    </span>
+<span class="c1">#    two_v</span>
+<span class="c1">#    </span>
+<span class="c1">#    two_v_colourbars</span>
+<span class="c1">#    </span>
+<span class="c1">#    three_h</span>
+<span class="c1">#    </span>
+<span class="c1">#    three_h_colourbars</span>
+<span class="c1">#    </span>
+<span class="c1">#    three_square</span>
+<span class="c1">#    </span>
+<span class="c1">#    three_square_colourbars</span>
+<span class="c1">#    </span>
+<span class="c1">#    four_square</span>
+<span class="c1">#    </span>
+<span class="c1">#    four_square_colourbars</span>
+<span class="c1">#&quot;&quot;&quot;</span>
+
 <span class="kn">import</span> <span class="nn">matplotlib.pyplot</span> <span class="k">as</span> <span class="nn">plt</span>
 <span class="kn">from</span> <span class="nn">matplotlib.gridspec</span> <span class="kn">import</span> <span class="n">GridSpec</span>
 <span class="kn">import</span> <span class="nn">tp</span>

diff --git a/docs/_modules/tp/calculate.html b/docs/_modules/tp/calculate.html
@@ -44,7 +44,7 @@
 <li class="toctree-l1"><a class="reference internal" href="../../index.html#contributors">Contributors</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../../index.html#license">License</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../../index.html#requirements">Requirements</a></li>
-<li class="toctree-l1"><a class="reference internal" href="../../modules.html">Python Package</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../../modules.html">Python API</a></li>
 </ul>
 
         </div>
@@ -73,53 +73,54 @@
            <div itemprop="articleBody">
 
   <h1>Source code for tp.calculate</h1><div class="highlight"><pre>
-<span></span><span class="sd">&quot;&quot;&quot;Calculates stuff.</span>
+<span></span><span class="sd">&quot;&quot;&quot;Calculates quantities used in other modules.</span>
 
 <span class="sd">Uses tp units by default, but can read the tprc.yaml to customise.</span>
-
-<span class="sd">Functions</span>
-<span class="sd">---------</span>
-
-<span class="sd">    cumulate:</span>
-<span class="sd">        sorts and cumulates.</span>
-<span class="sd">    gaussian:</span>
-<span class="sd">        gaussian distribution of height 1.</span>
-<span class="sd">    lorentzian:</span>
-<span class="sd">        area conserved lorentzian distribution.</span>
-<span class="sd">    lifetime:</span>
-<span class="sd">        particle lifetime.</span>
-<span class="sd">    mfp:</span>
-<span class="sd">        particle mean free path.</span>
-<span class="sd">    fd_occupation:</span>
-<span class="sd">        fermion occupation.</span>
-<span class="sd">    be_occupation:</span>
-<span class="sd">        boson occupation.</span>
-<span class="sd">    dfdde:</span>
-<span class="sd">        derivative of the Fermi-Dirac distribution.</span>
-<span class="sd">    thermal_conductivity:</span>
-<span class="sd">        total thermal conductivity.</span>
-<span class="sd">    power_factor:</span>
-<span class="sd">        power factor.</span>
-<span class="sd">    zt:</span>
-<span class="sd">        ZT.</span>
-<span class="sd">    kl:</span>
-<span class="sd">        lattice thermal conductivity for target ZT.</span>
-
-<span class="sd">    power_factor_fromdict:</span>
-<span class="sd">        adds power factor to dictionary.</span>
-<span class="sd">    zt_fromdict:</span>
-<span class="sd">        adds zt to dictionary.</span>
-<span class="sd">    kl_fromdict:</span>
-<span class="sd">        adds lattice thermal conductivity for target ZT to dictionary.</span>
-
-<span class="sd">    to_tp:</span>
-<span class="sd">        converts quantities to tp defaults from tprc.yaml.</span>
-<span class="sd">    from_tp:</span>
-<span class="sd">        converts quantities from tp defaults from tprc.yaml.</span>
-<span class="sd">    interpolate:</span>
-<span class="sd">        shrinks to smallest data size and interpolates.</span>
 <span class="sd">&quot;&quot;&quot;</span>
 
+<span class="c1">#Functions</span>
+<span class="c1">#---------</span>
+<span class="c1">#</span>
+<span class="c1">#    cumulate:</span>
+<span class="c1">#        sorts and cumulates.</span>
+<span class="c1">#    gaussian:</span>
+<span class="c1">#        gaussian distribution of height 1.</span>
+<span class="c1">#    lorentzian:</span>
+<span class="c1">#        area conserved lorentzian distribution.</span>
+<span class="c1">#    lifetime:</span>
+<span class="c1">#        particle lifetime.</span>
+<span class="c1">#    mfp:</span>
+<span class="c1">#        particle mean free path.</span>
+<span class="c1">#    fd_occupation:</span>
+<span class="c1">#        fermion occupation.</span>
+<span class="c1">#    be_occupation:</span>
+<span class="c1">#        boson occupation.</span>
+<span class="c1">#    dfdde:</span>
+<span class="c1">#        derivative of the Fermi-Dirac distribution.</span>
+<span class="c1">#    thermal_conductivity:</span>
+<span class="c1">#        total thermal conductivity.</span>
+<span class="c1">#    power_factor:</span>
+<span class="c1">#        power factor.</span>
+<span class="c1">#    zt:</span>
+<span class="c1">#        ZT.</span>
+<span class="c1">#    kl:</span>
+<span class="c1">#        lattice thermal conductivity for target ZT.</span>
+<span class="c1">#</span>
+<span class="c1">#    power_factor_fromdict:</span>
+<span class="c1">#        adds power factor to dictionary.</span>
+<span class="c1">#    zt_fromdict:</span>
+<span class="c1">#        adds zt to dictionary.</span>
+<span class="c1">#    kl_fromdict:</span>
+<span class="c1">#        adds lattice thermal conductivity for target ZT to dictionary.</span>
+<span class="c1">#</span>
+<span class="c1">#    to_tp:</span>
+<span class="c1">#        converts quantities to tp defaults from tprc.yaml.</span>
+<span class="c1">#    from_tp:</span>
+<span class="c1">#        converts quantities from tp defaults from tprc.yaml.</span>
+<span class="c1">#    interpolate:</span>
+<span class="c1">#        shrinks to smallest data size and interpolates.</span>
+<span class="c1">#&quot;&quot;&quot;</span>
+
 <span class="kn">import</span> <span class="nn">numpy</span> <span class="k">as</span> <span class="nn">np</span>
 <span class="kn">import</span> <span class="nn">tp</span>
 <span class="kn">from</span> <span class="nn">scipy.constants</span> <span class="kn">import</span> <span class="n">physical_constants</span>